SpikeList-class            package:CALIB            R Documentation

_C_l_a_s_s "_S_p_i_k_e_L_i_s_t" - _S_p_i_k_e _I_n_t_e_n_s_i_t_y _a_n_d _C_o_n_c_e_n_t_r_a_t_i_o_n _L_i_s_t

_D_e_s_c_r_i_p_t_i_o_n:

     A simple list-based class for storing red and green channel
     foreground and background intensities, spot area and
     concentrations for external control spike on spotted microarray.

_O_b_j_e_c_t_s _f_r_o_m _t_h_e _C_l_a_s_s:

     Objects can be created by calls of the form 'new("SpikeList",
     spike)' where spike is a list. In the CALIB package, SpikeList
     objects are normally generated by function  'read.spike'.

_L_i_s_t _C_o_m_p_o_n_e_n_t_s:

     Objects should contain the following list components:

     '_R': numeric matrix containing the red(Cy5) foreground intensities
          of all external control spikes on arrays. Rows correspond to
          spikes and  columns to arrays.

     '_G': numeric matrix containing the green(Cy3) foreground
          intensities of all external control spikes on arrays. 

     '_R_b': numeric matrix containing the red(Cy5) background
          intensities of all external control spikes on arrays. 

     '_G_b': numeric matrix containing the green(Cy3) background
          intensities of all external control spikes on arrays. 

     '_R_A_r_e_a': numeric matrix containing the red(Cy5) spot areas of all 
          external control spikes on arrays. 

     '_G_A_r_e_a': numeric matrix containing the green(Cy3) spot areas of
          all  external control spikes on arrays. 

     '_R_C_o_n_c': numeric matrix containing the red(Cy5) known
          concentrations of all external control spikes on arrays.

     '_G_C_o_n_c': numeric matrix containing the green(Cy3) know
          concentrations of all external control spikes on arrays.

     '_g_e_n_e_s': data.frame containing information on spikes spotted on
          the arrays. Should include a character column Name containing
          names for all the spikes.

     All of the matrices should have the same dimensions.

_E_x_t_e_n_d_s:

     Class '"list"', from data part. Class '"vector"', by class
     '"list"'.

_M_e_t_h_o_d_s:

     This class inherits directly from class List, so any operation
     appropriate for lists will work on objects of this class. In
     addition, SpikeList objects can be 'subsetted', 'combined' and
     'merged'. SpikeList objects will return dimensions and hence
     functions such as 'dim', 'dimnames', 'nrow' and 'ncol' are
     defined. Generic method 'show' is applied on 'SpikeList', so
     SpikeList will print in a compact way.

     SpikeList objects are used on functions such as
     'estimateParameter' or on some other data visualization functions
     like 'plotSpikeHI' in the CALIB package.

_A_u_t_h_o_r(_s):

     Hui Zhao

_R_e_f_e_r_e_n_c_e_s:

     the limma package

_S_e_e _A_l_s_o:

     'RGList_CALIB'.

     'RGList' in limma package.

